A fundamental problem in the mapping of mammalian genomes is the shear number of polymorphic markers required to achieve high resolution. Methods that simultaneously track multiple markers offer a major economy in surmounting this obstacle. We have been investigating the use of oligonucleotides derived from the interspersed repeat, LINE-1, for gene mapping in Mus domesticus/Mus spretus interspecific hybrids. Oligonucleotide hybridization probes that detect up to 14,000 insertion dimorphisms between these two sub-species are demonstrated. Oligonucleotides that specifically detect interspersed repeats in either Mus spretus or Mus domesticus have been developed. Oligonucleotides are available that detect the same set of insertion polymorphisms, and therefore can be used in combination to reinforce specificity. It is proposed to use these species- and polymorphism-specific probes for the saturation mapping of a 10-30 centimorgan region in a Mus spretus/Mus domesticus interspecific congenic strain. A variation of this method is proposed to extract markers linked to a target gene from a small panel of mice backcrossed only to the third generation. Direct Southern blotting with the most spretus-specific probe available shows 2000 copies in Mus spretus and only 6 copies in Mus domesticus. It is proposed to utilize Southern blots to directly map LINE-1 elements from this set. Finally, it is proposed to use the species-specific oligonucleotides as primers for direct PCR mapping.